GapMind for catabolism of small carbon sources

 

D-mannitol catabolism in Escherichia coli BW25113

Best path

gutB, gutE, gutA, mtlD

Also see fitness data for the top candidates

Rules

Overview: Mannitol degradation in GapMind is based on MetaCyc pathway mannitol degradation I via a phosphotransferase system (link), pathway II via mannitol 1-dehydrogenase (link), or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318).

17 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
gutB mannitol PTS system, EII-A component GutB b2704
gutE mannitol PTS system, EII-BC1 component GutE b2703
gutA mannitol PTS system, EII-C2 component GutA b2702
mtlD mannitol-1-phosphate 5-dehydrogenase b3600 b4465
Alternative steps:
cmtA mannitol phosphotransferase system, EII-CB component CmtA/MtlF b2933 b3599
cmtB mannitol phosphotransferase system, EII-A component CmtB/MtlF b2934 b3599
mak mannose kinase b0394 b1119
manA mannose-6-phosphate isomerase b1613 b2049
mt1d mannitol 1-dehydrogenase b0325 b4269
mt2d mannitol 2-dehydrogenase b2172 b1542
mtlA mannitol phosphotransferase system, EII-CBA components b3599 b2933
mtlE polyol ABC transporter, substrate-binding component MtlE/SmoE
mtlF polyol ABC transporter, permease component 1 (MtlF/SmoF) b1311
mtlG polyol ABC transporter, permease component 2 (MtlG/SmoG) b1312 b4032
mtlK polyol ABC transporter, ATP component MtlK/SmoG b4035 b3450
PLT5 polyol transporter PLT5
scrK fructokinase b0394 b1119

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory